16_tributary_detection_efficiencies
Markus Min
2022-10-10
Description
This Rmd file will go through the various tributaries in our model and model the detection efficiency at the most downstream interrogation site in each. It will also address the changing distribution of active arrays over time, and determine when a) detections in the tributaries are impossible; b) when it is not possible to calculate detection efficiency in the tributary; and c) when the most downstream (closest to the confluence) site had significant changes in detection capability.
Note: Shelby calculated annual detection efficiencies for some years for the following 11 tributaries:
- Hood River
- Fifteenmile Creek
- Deschutes River
- John Day River
- Umatilla River
- Walla Walla River
- Yakima River
- Wenatchee River
- Entiat River
- Tucannon River
- Imnaha River
Summary
The 17 tributaries in our model can broadly be organized into multiple groups:
1) Tributaries where detection efficiencies can be estimated at a site near the mouth for some years
- Asotin Creek (2011-)
- Deschutes River (2013-2019)
- Entiat River (2007-)
- Fifteenmile Creek (2011-2019) - note river mouth array still active, but no upstream arrays active starting July 2019
- Hood River (2015-). NOTE: river mouth site is active since 2012, but we have no detections at upstream sites until 2015
- Tucannon River (2006-)
- Umatilla River (2007-)
- Wenatchee River (2010-)
2) Tributaries with a array on the mainstem, but a bit up from the mouth
- Imnaha River (2011-) - at RKM 7 and 10
- John Day River (2012-) - at RKM 32. NOTE: River mouth site active since 2007, but no detections at upstream sites until 2012.
- Methow River - at RKM 3 (2009-2017); at RKM 8 (2017-)
- Okanogan River (2013-) - at RKM 25
- Walla Walla River - at RKM 9 and 10, then at RKM 5 starting in 2019
- Yakima River (2005-) at RKM 76
3) Tributaries without anything close to a river mouth site, but plenty of others
- Clearwater River
- Salmon River
4) Tributaries that we should likely remove from the model given the paucity of arrays
- Grande Ronde River
Note: The difference between those listed under (3) and those listed under (4) is just how many arrays there are. This shows up in the probabilities of movement from the mainstem to the tributaries for fish of that origin. For example:
- Clearwater River from upstream of LGR: 0.303
- Salmon River from upstream of LGR: 0.279
- Grande Ronde from upstream of LGR: 0.084
Tributary flow data
Tributary flow data was found using DART: https://www.cbr.washington.edu/dart/query/streamflow_daily. Tributary data was then queried directly from USGS by finding the site on the interactive USGS dashboard (https://dashboard.waterdata.usgs.gov/app/nwd/lang-en/?aoi=default) and navigating to the data page for the specific site. I then selected daily data for discharge and gage height.
On the USGS data page for each, I then queried 2005-01-01 through 2022-10-17 and saved the page source of the table of tab-separated values.
For each tributary, I selected data from the station closest to the river mouth array.
Detection efficiency GLM
In this Rmd, we estimate annual detection efficiency as a function of equipment configuration and discharge.
The equation for estimating detection efficiency is as follows: \[ z_i \sim \text{Binomial}(p_{i}) \\ \text{logit}(p_i) = \alpha_{j, k} + \beta_{j, k} discharge_{j,t} \] The indices represent the following:
- \(i\) is the individual fish
- \(j\) is the tributary
- \(k\) is the site configuration (a categorical variable)
- \(t\) is the run year
Asotin Creek
Site overview
- ACM - Asotin Creek near mouth is at RKM 1 of Asotin Creek; others are at RKM 5, 22, and 25
- ACM start date 8/1/2011. Run year 11/12 and onwards can be seen in Asotin Creek
- Other sites have start dates within a week in early August 2009. However, these all exist upstream of the Georges Creek confluence, which could be an issue.
## event_site_name Int.Site.Start.Date Int.Site.End.Date
## 1 ACM - Asotin Creek near mouth 8/1/2011
## 2 ACB - Asotin Cr. at Cloverland Brdg. 7/30/2009
## 3 CCA - Lower Charley Creek ISA 8/7/2009
## 4 AFC - No./So. Fk Asotin Cr. Jct. ISA 7/30/2009
## Interrogation.Site.Location.RKM
## 1 522.234.001
## 2 522.234.005
## 3 522.234.022.001
## 4 522.234.025Is there reason to believe that the detection efficiency of the antennas at the river mouth site may have changed over time?
Yes - upgrade on 10/12/2018. At least two eras:
- 8/1/2011-10/11/2018 (potentially different starting 9/21/12, since two antennas were added to site on this date)
- 10/12/2018-present
ACM description from PTAGIS:
ACM is a permanent instream PIT tag interrogation site located near the mouth of Asotin Creek, a tributary of the Snake River. As of 10/12/2018 all previous components present at ACM have been replaced and upgraded. The site consists of 3 rows of antennas with each row containing two 20- foot HDPE antennae, installed in flat-plate configuration. Each antenna is powered by a Biomark IS1001 (ACN) and the ACNs are connected to a Biomark IS1001-MTS master controller. The antennas were built and installed by WDFW. The site is connected to grid power to charge the battery bank powering the detection system. A cellular modem is installed on site to provide remote communication and allow for automated data collection, however, only manual data collection from the IS1001-MTS will occur at ACM until further notice. Prior to the upgrade, the site consisted of six antennas powered by an FS1001M.
ACM operational history notes from PTAGIS
- Site down from March 19 - August 26, 2017
- Site down March 25-September 1, 2014
- Site down from March 26 - August 30, 2012. Two antennas were added to the site on September 21, 2012.
Detection efficiency
| year | missed_det | total | det_eff | det_eff_lower95 | det_eff_upper95 |
|---|---|---|---|---|---|
| 2011 | 0 | 4 | 1.000 | 0.398 | 1.000 |
| 2012 | 7 | 41 | 0.829 | 0.679 | 0.928 |
| 2013 | 3 | 30 | 0.900 | 0.735 | 0.979 |
| 2014 | 10 | 40 | 0.750 | 0.588 | 0.873 |
| 2015 | 23 | 44 | 0.477 | 0.325 | 0.633 |
| 2016 | 15 | 21 | 0.286 | 0.113 | 0.522 |
| 2017 | 7 | 11 | 0.364 | 0.109 | 0.692 |
| 2018 | 2 | 4 | 0.500 | 0.068 | 0.932 |
| 2019 | 0 | 1 | 1.000 | 0.025 | 1.000 |
| 2020 | 0 | 8 | 1.000 | 0.631 | 1.000 |
| 2021 | 0 | 13 | 1.000 | 0.753 | 1.000 |
| 2022 | 0 | 4 | 1.000 | 0.398 | 1.000 |
| Total | 67 | 221 | 0.697 | 0.632 | 0.757 |
USGS data
- I don’t see any data on CBR dart, but there is data on USGS.
Station: Asotin Creek at Asotin, WA. USGS 13335050 - discharge and gauge height
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## [[3]]
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## [[4]]## Warning: Removed 32 rows containing missing values (geom_point).
Detection efficiency vs. discharge
det_eff_glm(variables = "discharge and gage height",
tributary_name = "Asotin Creek",
usgs_file_name = "asotin_creek_13335050.txt",
equipment_categories_start_run_years = c("11/12", "18/19"),
equipment_categories_end_run_years = c("17/18", "21/22"),
river_mouth_site = "ACM - Asotin Creek near mouth",
river_mouth_site_start_date = "2011-08-01",
river_mouth_site_end_date = "2023-01-01")## [[1]]
##
## Call:
## glm(formula = detected ~ era + mean_discharge_cfs, family = binomial(link = "logit"),
## data = trib_det_discharge)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.7206 -1.3265 0.7187 0.9539 1.0353
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -0.438353 0.529996 -0.827 0.4082
## era18/19-21/22 16.941417 775.807201 0.022 0.9826
## mean_discharge_cfs 0.012303 0.005863 2.098 0.0359 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 271.18 on 220 degrees of freedom
## Residual deviance: 246.27 on 218 degrees of freedom
## AIC: 252.27
##
## Number of Fisher Scoring iterations: 16
##
##
## [[2]]## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf
Clearwater River
There is no site near the mouth of the Clearwater River; in fact, there is not a single interrogation site on the mainstem Clearwater River.
## event_site_name Int.Site.Start.Date Int.Site.End.Date
## 1 LAP - Lapwai Creek, near its mouth 10/1/2008
## 2 SWT - Sweetwater Cr. near its mouth 8/1/2008
## 3 WEB - Webb Creek 11/17/2010
## 4 MIS - Mission Creek 12/23/2010 4/9/2019
## 5 JUL - Potlatch River near Juliaetta 10/2/2008 5/22/2013
## 6 KHS - Big Bear Cr. @ Kendrick HS 12/1/2007
## 7 BBA - Big Bear Creek Array 3/2/2018
## 8 PCM - Pine Creek Mouth, Potlatch R. 10/1/2015
## 9 EPR - East Fork Potlatch Array 10/25/2019
## 10 HLM - Potlatch River near Helmer 9/1/2009 5/22/2015
## 11 DWL - Dworshak NFH adult trap 2/1/2010
## 12 LC1 - Lower Lolo Creek at rkm 21 11/1/2011
## 13 LC2 - Upper Lolo Creek at rkm 25 11/1/2011
## 14 SC1 - Lower SF Clearwater R at rkm 1 8/18/2011
## 15 SC2 - Lower SF Clearwater R at rkm 2 9/19/2011
## 16 CLC - Clear Creek near Kooskia NFH 2/11/2015 7/23/2018
## 17 LRL - Lower Lochsa River Array Site 10/10/2016
## 18 LRU - Lochsa River Upper Site 12/5/2017
## 19 CRT - Crooked River Satellite Fac. 1/5/2012 7/29/2015
## Interrogation.Site.Location.RKM
## 1 522.224.019.001
## 2 522.224.019.010.001
## 3 522.224.019.010.006.001
## 4 522.224.019.016.001
## 5 522.224.024.014
## 6 522.224.024.023.000
## 7 522.224.024.023.002
## 8 522.224.024.028.001
## 9 522.224.024.065.003
## 10 522.224.024.066
## 11 522.224.065
## 12 522.224.087.021
## 13 522.224.087.025
## 14 522.224.120.001
## 15 522.224.120.002
## 16 522.224.120.004.001
## 17 522.224.120.037.001
## 18 522.224.120.037.003
## 19 522.224.120.094.001Is there reason to believe that the detection efficiency of the antennas at the river mouth site may have changed over time?
NA - no river mouth site chosen
Deschutes River
The Deschutes River Mouth (DRM) array was active for run years 13/14 through 18/19 (3/13/2013 - 8/9/2019). In all other years, antennas were only found at RKM 69 or greater.
## event_site_name Int.Site.Start.Date Int.Site.End.Date
## 1 DRM - Deschutes River mouth 3/13/2013 8/9/2019
## 2 DBH - Buck Hollow Ck Deschutes Trib 4/2/2012
## 3 DSF - Deschutes Sherars Falls 10/27/2016
## 4 DBO - Bakeoven Ck Deschutes Trib 4/5/2012
## 5 WSR - Warm Springs River PIT Array 8/10/2014
## 6 WSH - Warm Springs Hatchery 2/1/2008
## 7 TR1 - Lower Trout Cr - Deschutes 12/1/2012
## 8 TR2 - Trout/Antelope Cr - Deschutes 11/1/2013
## 9 SHK - Shitike Creek PIT Array 2/24/2014
## Interrogation.Site.Location.RKM
## 1 328.001
## 2 328.069.001
## 3 328.071
## 4 328.083.001
## 5 328.135.001
## 6 328.135.016
## 7 328.140.001
## 8 328.140.021
## 9 328.155.001Is there reason to believe that the detection efficiency of the antennas at the river mouth site may have changed over time?
No - single era. Note that the detection efficiencies for DRM calculated by Shelby in 13/14 and 14/15 are 47.0% (SE 4.7%) and 41.4% (SE 6.5%), respectively. No notes in operational history.
DRM description from PTAGIS:
In February-March 2013, two antenna arrays, arranged upstream- downstream from one another, were installed just upstream from the mouth of the Deschutes River in the west channel at Moody Island (rkm 0.46). This system is based on Biomark?s new IS1001-MTS Multiplexing Transceiver System. The arrays consist of 12-Biomark 20ft STOUT antennas, each controlled by a submersible IS1001 antenna control nodes. There are seven antennas in the upstream array and 60 feet downstream are five antennas in the downstream array. The IS1001 nodes are connected in series and they in turn are connected to an IS1001-Master Controller located adjacent to the array on the west bank of the Deschutes River. Diagnostic and tag detection data will be retrieved remotely using a Campbell Scientific CR1000 data logger and cell phone connection. The IS1001-MTS is capable of detecting FDX-B and HDX PIT tags. Site is no longer active.
DRM operational history notes from PTAGIS
Nothing of note.
Detection efficiency
| year | missed_det | total | det_eff | det_eff_lower95 | det_eff_upper95 |
|---|---|---|---|---|---|
| 2013 | 18 | 65 | 0.723 | 0.598 | 0.827 |
| 2014 | 62 | 91 | 0.319 | 0.225 | 0.425 |
| 2015 | 30 | 44 | 0.318 | 0.186 | 0.476 |
| 2016 | 29 | 37 | 0.216 | 0.098 | 0.382 |
| 2017 | 26 | 34 | 0.235 | 0.107 | 0.412 |
| 2018 | 15 | 31 | 0.516 | 0.331 | 0.698 |
| 2019 | 7 | 7 | 0.000 | 0.000 | 0.410 |
| Total | 187 | 309 | 0.395 | 0.340 | 0.452 |
USGS data
Station: Deschutes River at Moody, Near Biggs, OR USGS 14103000 - discharge only
## [[1]]
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## [[2]]
Detection efficiency vs. discharge
det_eff_glm(variables = "discharge only",
tributary_name = "Deschutes River",
usgs_file_name = "deschutes_river_14103000.txt",
equipment_categories_start_run_years = NA,
equipment_categories_end_run_years = NA,
river_mouth_site = "DRM - Deschutes River mouth",
river_mouth_site_start_date = "2013-03-13",
river_mouth_site_end_date = "2019-08-09")## [[1]]
##
## Call:
## glm(formula = detected ~ mean_discharge_cfs, family = binomial(link = "logit"),
## data = trib_det_discharge)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.125 -1.012 -0.945 1.324 1.438
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -3.7416710 3.0676205 -1.220 0.223
## mean_discharge_cfs 0.0005880 0.0005435 1.082 0.279
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 414.59 on 308 degrees of freedom
## Residual deviance: 413.42 on 307 degrees of freedom
## AIC: 417.42
##
## Number of Fisher Scoring iterations: 4
##
##
## [[2]]
Entiat River
- Lower Entiat River (ENL) site is at RKM 2; active since 2007
## event_site_name Int.Site.Start.Date Int.Site.End.Date
## 1 ENL - Lower Entiat River 10/1/2007
## 2 PD1 - Top of Chelan PUD side channel 4/3/2012 6/14/2013
## 3 PD2 - Bot of Chelan PUD side channel 4/3/2012 6/6/2013
## 4 HN1 - Top of Harrison side channel 3/27/2013 12/29/2016
## 5 HN3 - Bottom Harrison Side Channel 3/27/2013 4/22/2017
## 6 HN2 - Middle Harrison Side Channel 4/2/2013 4/22/2017
## 7 SR2 - Bot of Entiat R side channel 10/6/2011 1/9/2017
## 8 SR1 - Top of Entiat R side channel 10/6/2011 3/6/2017
## 9 RCT - Roaring Creek Temporary Array 3/1/2011
## 10 URT - Upper Roaring Temporary Array 3/1/2011 5/23/2012
## 11 HS1 - Top of side channel near ENFH 7/11/2015 12/15/2016
## 12 HS2 - Bottom side channel near ENFH 7/11/2015 12/16/2016
## 13 WL2 - Bottom of Wilson Creek channel 10/11/2011 3/22/2017
## 14 ENA - Upper Entiat River at rkm 17.1 4/6/2011
## 15 MAD - Mad River, Entiat River Basin 10/1/2007
## 16 TLT - Tillicum Creek Temporary Array 3/1/2011 6/5/2014
## 17 UMR - Upper Mad Rv. Temporary Array 3/1/2011 5/13/2012
## 18 ENM - Middle Entiat River 3/1/2008 10/31/2018
## 19 ENS - Upper Entiat River at rkm 35.7 5/5/2011 8/20/2019
## 20 TY1 - Low Flow Top of Tyee Channel 9/3/2013 6/27/2015
## 21 ENF - Upper Entiat River at rkm 40.6 8/10/2010
## 22 3D4 - Bottom of 3D Side Channel 3/27/2013 1/13/2017
## 23 3D1 - Top of 3D Side Channel 3/27/2013 3/7/2017
## 24 3D3 - Middle-2 of 3D Side Channel 3/27/2013 1/6/2017
## Interrogation.Site.Location.RKM
## 1 778.002
## 2 778.005
## 3 778.005
## 4 778.006
## 5 778.006
## 6 778.006
## 7 778.007
## 8 778.007
## 9 778.010.001
## 10 778.010.002
## 11 778.011
## 12 778.011
## 13 778.011
## 14 778.017
## 15 778.017.001
## 16 778.017.003.001
## 17 778.017.011
## 18 778.026
## 19 778.036
## 20 778.038
## 21 778.041
## 22 778.043
## 23 778.043
## 24 778.043Is there reason to believe that the detection efficiency of the antennas at the river mouth site may have changed over time?
Appears to be a single era, despite 15 years of operation. However, from 2008-2011, there were large periods of time in which the site was not operational, and antennas were frequently replaced as they went down. Shelby calculated detection efficiencies for ENL starting in 09/10 - values are all basically within SE of each other above 90% (no significant year-to-year variation).
ENL description from PTAGIS:
This site is located immediately upstream of Entiat, WA. The site is grid powered with a battery switcher and includes eight HDPE pipe-style antennas and IS1001 readers. The readers are connected to an IS1001-MC and satellite remote communications.
ENL operational history notes from PTAGIS
- 2008: April 16 - 18: data lost due to buffer overrun. May 25 - July 24: all antennae washed out. Sept. 8 - 24: no data due to MUX board failure.
- 2009: Jan. 7 - Mar. 7: all antennae washed out. May 26 - July 9: site not operational due to elevated flows.
- 2010: The site operated continually from January 1st until May 2, when elevated river discharge resulted in the operational loss of antenna #23. This was followed by the loss of antenna #22 on May 16, #21 on May 31, #25 on June 5, #24 on June 8, and #26 on June 13. There was no detection capability and ENL from June 13 until July 28, when antennas 21, 22, 23, 24, and 25 were reinstalled.
- 2011: Antennas 3, 5, 6 lost power Jan. 19, antennas 2 and 4 have high noise, antenna 1 has intermittent high noise. Antennas 1,2, and 4 not reading tags due to high noise on Jan. 27. Antennas 3, 5, and 6 were replaced on Feb. 10, and the noise was reduced on antennas 1, 2, and 4. Periods of high noise occurred during May. Antennas 3 and 6 not operational as of May 23; antenna 5 not operational on June 13. Antennas 3, 5, and 6 replaced on September 1. Site down from October 5-11. Antenna 1 lost power from October 27-December 6.
Detection efficiency
| year | missed_det | total | det_eff | det_eff_lower95 | det_eff_upper95 |
|---|---|---|---|---|---|
| 2008 | 1 | 4 | 0.750 | 0.194 | 0.994 |
| 2009 | 0 | 9 | 1.000 | 0.664 | 1.000 |
| 2010 | 5 | 39 | 0.872 | 0.726 | 0.957 |
| 2011 | 2 | 43 | 0.953 | 0.842 | 0.994 |
| 2012 | 4 | 31 | 0.871 | 0.702 | 0.964 |
| 2013 | 3 | 30 | 0.900 | 0.735 | 0.979 |
| 2014 | 1 | 38 | 0.974 | 0.862 | 0.999 |
| 2015 | 3 | 23 | 0.870 | 0.664 | 0.972 |
| 2016 | 6 | 28 | 0.786 | 0.590 | 0.917 |
| 2017 | 3 | 21 | 0.857 | 0.637 | 0.970 |
| 2018 | 0 | 8 | 1.000 | 0.631 | 1.000 |
| 2019 | 1 | 8 | 0.875 | 0.473 | 0.997 |
| 2020 | 1 | 10 | 0.900 | 0.555 | 0.997 |
| 2021 | 0 | 7 | 1.000 | 0.590 | 1.000 |
| 2022 | 0 | 2 | 1.000 | 0.158 | 1.000 |
| Total | 30 | 301 | 0.900 | 0.861 | 0.932 |
USGS data
Station: Entiat River Near Entiat, WA USGS 12452990 - discharge and gage height
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## [[2]]
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## [[3]]
##
## [[4]]## Warning: Removed 166 rows containing missing values (geom_point).
Detection efficiency vs. discharge
det_eff_glm(variables = "discharge and gage height",
tributary_name = "Entiat River",
usgs_file_name = "entiat_river_12452990.txt",
equipment_categories_start_run_years = NA,
equipment_categories_end_run_years = NA,
river_mouth_site = "ENL - Lower Entiat River",
river_mouth_site_start_date = "2007-10-01",
river_mouth_site_end_date = "2023-01-01")## [[1]]
##
## Call:
## glm(formula = detected ~ mean_discharge_cfs, family = binomial(link = "logit"),
## data = trib_det_discharge)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -2.1508 0.4576 0.4577 0.4592 0.4599
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 2.175e+00 1.127e+00 1.930 0.0536 .
## mean_discharge_cfs 5.048e-05 2.153e-03 0.023 0.9813
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 195.26 on 300 degrees of freedom
## Residual deviance: 195.26 on 299 degrees of freedom
## AIC: 199.26
##
## Number of Fisher Scoring iterations: 4
##
##
## [[2]]
Fifteenmile Creek
- 158 is ar RKM 4, active since Nov 2011. Only two upstream sites, one of which was only active through 6/30/2019.
## event_site_name Int.Site.Start.Date Int.Site.End.Date
## 1 158 - Fifteenmile Ck at Eightmile Ck 11/29/2011
## 2 15D - Fifteenmile Ck at Dry Ck 3/15/2012 6/30/2019
## 3 15R - Fifteenmile Ck at Ramsey Ck 5/10/2011 4/4/2018
## Interrogation.Site.Location.RKM
## 1 309.004
## 2 309.038
## 3 309.056Is there reason to believe that the detection efficiency of the antennas at the river mouth site may have changed over time?
Short periods of time in which antennas were active. Shelby calculated efficiencies starting in 12/13: 49.8% (SE 10.1%), 100% (no SE), 100% (no SE). Doesn’t appear that antennas being down affected it.
158 description from PTAGIS:
INSTREAM DETECTION ARRAY AT THE CONFLUENCE OF EIGHTMILE CREEK AND FIFTEENMILE CREEKS, CONSISTING OF A FS1001M MULTIPLEXING TRANCEIVER, CELL MODEM, AND THREE ANTENNAS IN EACH CREEK. ANTENNA ARRAYS FOR EACH CREEK CONSIST OF ONE ANTENNA EACH THAT SPANS THE NORMAL HIGH WATER MARK AND IS SECURED TO THE SUBSTRATE FOR PASS-OVER DETECTION. SITE IS GRID-POWERED AND OPERATES YEAR-ROUND. SITE IS ON PRIVATE LAND.
158 operational history notes from PTAGIS
- 2012: Antenna 4 down from March 31 - April 5. Antenna 6 down from March 31 - April 18.
- 2013: Antenna 6 down from October 23 - December 27
- 2014: Site down intermittently through the year, check event log for details. Converted to IS1001-MTS system in October. MARKUS NOTE: there is no event log for 2014, would have to email contact to get it.
Detection efficiency
| year | missed_det | total | det_eff | det_eff_lower95 | det_eff_upper95 |
|---|---|---|---|---|---|
| 2012 | 1 | 20 | 0.950 | 0.751 | 0.999 |
| 2013 | 0 | 3 | 1.000 | 0.292 | 1.000 |
| 2014 | 0 | 6 | 1.000 | 0.541 | 1.000 |
| 2015 | 0 | 8 | 1.000 | 0.631 | 1.000 |
| 2016 | 0 | 5 | 1.000 | 0.478 | 1.000 |
| 2017 | 0 | 4 | 1.000 | 0.398 | 1.000 |
| 2018 | 2 | 10 | 0.800 | 0.444 | 0.975 |
| Total | 3 | 56 | 0.946 | 0.851 | 0.989 |
USGS data
NO USGS DATA
Grande Ronde River
The Grande Ronde is basically hopeless - we might consider removing it from our model. The first mainstem site on the Grande Ronde is at RKM 155.
## event_site_name Int.Site.Start.Date Int.Site.End.Date
## 1 JOC - Joseph Creek ISA @ km 3 10/1/2010
## 2 WEN - Wenaha River Mouth 9/27/2018
## 3 WR1 - Wallowa River at river km 14 8/16/2013
## 4 MR1 - Minam River at river km 0.5 2/20/2020
## 5 WR2 - Wallowa River at rkm 32 8/2/2018
## 6 UGR - Upper Grande Ronde at rkm 155 10/18/2012
## 7 CCU - Catherine Creek at Union 12/19/2018
## 8 CCW - Catherine Creek Ladder/Weir 3/2/2015
## 9 UGS - Upper Grande Ronde Starkey 11/3/2017
## Interrogation.Site.Location.RKM
## 1 522.271.007.003
## 2 522.271.073.001
## 3 522.271.131.014
## 4 522.271.131.016.001
## 5 522.271.131.032
## 6 522.271.155
## 7 522.271.232.025
## 8 522.271.232.032
## 9 522.271.291Hood River
HRM site is at RKM 1, starting in January 2012.
## event_site_name Int.Site.Start.Date Int.Site.End.Date
## 1 HRM - Hood River Mouth 1/9/2012
## 2 MVF - Moving Falls Fish Ladder 7/29/2015
## 3 EFD - East Fork Diversion Fishway 3/9/2016
## 4 SND - Sandtrap Acclimation Site 4/30/2018 5/7/2020
## Interrogation.Site.Location.RKM
## 1 273.000
## 2 273.020.004
## 3 273.023.011
## 4 273.023.033Is there reason to believe that the detection efficiency of the antennas at the river mouth site may have changed over time?
The description indicates that this site is highly influenced by river stage. Shelby calculated detection efficiencies in 12/13 and 13/14 of 65% (SE 6.5%) and 41.6% (SE 9.8%), respectively. So yes, I think we should look into annual detection efficiencies, but I also don’t think that there is a directional trend/regime shift/multiple eras. According to PTAGIS, there were no upstream sites prior to August 2015. So how did Shelby calculate detection efficiencies in 12/13 and 13/14 for HRM?
HRM description from PTAGIS:
An instream interrogation system consisting of 2 antenna arrays located at the mouth of the Hood River. The antennas are against the west side jetty just inside the bar where the Hood River meets the Columbia River. The upstream array is comprised of five 20 foot antennas covering a total of 100 feet from shore. The downstream array is comprised of two 20 foot antennas that extend 40 feet from shore. The antenna arrays cover approximately 3/4 the stream width at low water conditions and a half of the stream at bank full. The transceiver is a IS1001-MTS and power is provided by solar panels charging a battery bank. Interrogation data is submitted several times a week via cellular modem.
HRM operational history notes from PTAGIS
- 2015: Antenna 1 down April 15 - May 11. Antennas 2 and 3 down April 15 - June 5. All 3 upstream antennas replaced June 5 and new antenna added to downstream array.
- 2014: Site down September 30-October 27 for installation of new antennas and MTS transceiver.
- 2012: First year of operations. Site down a few times in November and December.
Detection Efficiency
| year | missed_det | total | det_eff | det_eff_lower95 | det_eff_upper95 |
|---|---|---|---|---|---|
| 2015 | 3 | 4 | 0.250 | 0.006 | 0.806 |
| 2016 | 8 | 12 | 0.333 | 0.099 | 0.651 |
| 2017 | 9 | 15 | 0.400 | 0.163 | 0.677 |
| 2018 | 10 | 28 | 0.643 | 0.441 | 0.814 |
| 2019 | 12 | 25 | 0.520 | 0.313 | 0.722 |
| 2020 | 12 | 14 | 0.143 | 0.018 | 0.428 |
| 2021 | 3 | 6 | 0.500 | 0.118 | 0.882 |
| 2022 | 4 | 5 | 0.200 | 0.005 | 0.716 |
| Total | 61 | 109 | 0.440 | 0.345 | 0.539 |
USGS data
Station: Hood River at Tucker Bridge, near Hood River, OR USGS 1412000 - this is a bit upstream of HRM site and before confluence with Whiskey Creek, but it should be good enough - discharge only
## [[1]]
##
## [[2]]
Detection efficiency vs. discharge
det_eff_glm(variables = "discharge only",
tributary_name = "Hood River",
usgs_file_name = "hood_river_14120000.txt",
equipment_categories_start_run_years = NA,
equipment_categories_end_run_years = NA,
river_mouth_site = "HRM - Hood River Mouth",
river_mouth_site_start_date = "2012-01-09",
river_mouth_site_end_date = "2023-01-01")## [[1]]
##
## Call:
## glm(formula = detected ~ mean_discharge_cfs, family = binomial(link = "logit"),
## data = trib_det_discharge)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.079 -1.078 -1.076 1.280 1.282
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -2.509e-01 9.902e-01 -0.253 0.800
## mean_discharge_cfs 1.281e-05 1.109e-03 0.012 0.991
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 149.55 on 108 degrees of freedom
## Residual deviance: 149.55 on 107 degrees of freedom
## AIC: 153.55
##
## Number of Fisher Scoring iterations: 3
##
##
## [[2]]
Imnaha River
There are two Imnaha River sites close to the river mouth, at RKM 7 (IR1) and RKM 10 (IR2), both starting in November/December 2010. Would we pool these? There is also a tributary downstream of these on Cow Creek, which flows into the Imnaha at RKM 6.
## event_site_name Int.Site.Start.Date Int.Site.End.Date
## 1 COC - Cow Creek ISA @ stream mouth 1/1/2011
## 2 IR1 - Lower Imnaha River ISA @ km 7 12/1/2010
## 3 IR2 - Lower Imnaha River ISA @ km 10 11/1/2010
## 4 CMP - Camp Creek at rkm 2 - Imnaha 2/15/2013
## 5 CMP - Camp Creek at rkm 2 - Imnaha 2/15/2013
## 6 BSC - Big Sheep Creek ISA at km 6 10/1/2010
## 7 IR3 - Upper Imnaha River ISA @ km 41 2/1/2011
## 8 GCM - Grouse Creek Mouth 3/18/2020
## 9 CZY - Crazyman Creek at 0.6 km 11/8/2013
## 10 IR4 - Imnaha Weir Downstream Array 8/18/2016
## 11 IR5 - Imnaha Weir Upstream Array 8/18/2016
## 12 IML - Imnaha River Weir Adult Ladder 5/18/2015
## Interrogation.Site.Location.RKM
## 1 522.308.006.001
## 2 522.308.007
## 3 522.308.010
## 4 522.308.032.002.002
## 5 522.308.032.002.002
## 6 522.308.032.006
## 7 522.308.041
## 8 522.308.066.000
## 9 522.308.080.001
## 10 522.308.084
## 11 522.308.084
## 12 522.308.084Is there reason to believe that the detection efficiency of the antennas at the river mouth site may have changed over time?
Nothing significant in site operational history. Shelby calculated detection efficiencies at IR1 for 11/12 through 14/15 - some fluctuation, between 84% and 100%, also variation between wild and hatchery populations.
IR1 description from PTAGIS:
In-stream detection system consisting of a single array located in the lower Imnaha River. The array (IR1) located at river km 7 (N 45.761162, W -116.750658) consists of four 20 foot Biomark flat panel antennas that span the entire river at base flow. IR1 is operated by the Integrated Status and Effectiveness Project (ISEMP) cooperators Nez Perce Tribe and Quantitative Consultants, Inc. and was installed for continuous monitoring on December 3, 2010. The array includes ISEMP standard site monitoring equipment including: air and water temperature probes, and a water pressure transducer to monitor stream level. Electrical power is provided by a solar/propane hybrid thermal electric generator and remote communication provided by a satellite modem.
IR1 operational history notes from PTAGIS
- 2011: High noise levels from January 11 - March 10.
IR2 description from PTAGIS:
In-stream detection system consisting of a single array located in the lower Imnaha River. The array (IR2) located at river km 10 (N 45.742839 W -116.764563) consists of one 10 foot and four 20 foot Biomark flat panel antennas that span the entire river at base flow. IR2 is operated by the Integrated Status and Effectiveness Project (ISEMP) cooperators Nez Perce Tribe and Quantitative Consultants, Inc. and was installed for continuous monitoring in November 2010. The array includes ISEMP standard site monitoring equipment including: air and water temperature probes, and a water pressure transducer to monitor stream level. Electrical power is provided by a solar/propane hybrid thermal electric generator and remote communication provided by a satellite modem.
IR2 operational history notes from PTAGIS
- 2011: High noise levels from January 31 - March 10 resulted in sporadic downtime.
Detection efficiency
| year | missed_det | total | det_eff | det_eff_lower95 | det_eff_upper95 |
|---|---|---|---|---|---|
| 2012 | 0 | 3 | 1.000 | 0.292 | 1.000 |
| 2013 | 3 | 100 | 0.970 | 0.915 | 0.994 |
| 2014 | 11 | 174 | 0.937 | 0.890 | 0.968 |
| 2015 | 9 | 211 | 0.957 | 0.921 | 0.980 |
| 2016 | 55 | 137 | 0.599 | 0.511 | 0.681 |
| 2017 | 4 | 58 | 0.931 | 0.833 | 0.981 |
| 2018 | 1 | 98 | 0.990 | 0.944 | 1.000 |
| 2019 | 4 | 63 | 0.937 | 0.845 | 0.982 |
| 2020 | 0 | 59 | 1.000 | 0.939 | 1.000 |
| 2021 | 0 | 75 | 1.000 | 0.952 | 1.000 |
| 2022 | 3 | 80 | 0.963 | 0.894 | 0.992 |
| Total | 90 | 1058 | 0.915 | 0.896 | 0.931 |
What happened in 2016??? There’s nothing in the logs, but perhaps it’s a river stage issue?
USGS data
Station: Imnaha River at Imnaha, OR USGS 13292000 - Site went offline 2013-10-22 - discharge only
## [[1]]
##
## [[2]]
Detection efficiency vs. discharge
det_eff_glm(variables = "discharge only",
tributary_name = "Imnaha River",
usgs_file_name = "imnaha_river_13292000.txt",
equipment_categories_start_run_years = NA,
equipment_categories_end_run_years = NA,
river_mouth_site = "IR1 - Lower Imnaha River ISA @ km 7",
river_mouth_site_start_date = "2012-12-01", river_mouth_site_end_date = "2023-01-01")## [[1]]
##
## Call:
## glm(formula = detected ~ mean_discharge_cfs, family = binomial(link = "logit"),
## data = trib_det_discharge)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -2.7341 0.2195 0.4056 0.4056 0.4056
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -0.614350 2.032466 -0.302 0.762
## mean_discharge_cfs 0.008835 0.005457 1.619 0.105
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 106.25 on 235 degrees of freedom
## Residual deviance: 102.86 on 234 degrees of freedom
## (822 observations deleted due to missingness)
## AIC: 106.86
##
## Number of Fisher Scoring iterations: 6
##
##
## [[2]]## Warning: Removed 8 rows containing missing values (geom_point).## Warning: Removed 8 rows containing missing values (geom_text_repel).
John Day River
- JD1 is the most downstream array, but it’s all the way at RKM 32.
- JD1 has a known change over time in detection efficiency. From Richins 2017: “A suspicious trend was observed for the John Day wild population (Figure A.3). The detection efficiencies at “JD1” from 2008/2009 to 2010/2011 were over 98%. According to the PTAGIS event log, the array was washed out by high flows in 2011. A new array was installed at the same location in 2012. In the following run years, the efficiencies dropped by more than half to 38.8%—48.8%. This shift in detection efficiencies was mirrored by a similar and opposite shift in estimates of return rate to home. Total success rates jumped from 34.7%—43.3% to 58.9%— 63.4%. This trend suggests that detection efficiencies may be overestimated in earlier years or underestimated in later years. However, spawning abundance of John Day River steelhead did increase in the same time period (Northwest Fisheries Science Center 2015).”
- Note: We have no upstream arrays until 2012. How did Shelby get detection efficiencies?
## event_site_name Int.Site.Start.Date Int.Site.End.Date
## 1 JD1 - John Day River, McDonald Ferry 9/1/2007
## 2 RCJ - Rock Creek John Day Basin 9/30/2014
## 3 30M - Thirtymile Crk John Day Basin 4/1/2016
## 4 BR0 - Bridge Creek Gauge 7/17/2012
## 5 BR1 - Bridge Creek Kiosk 7/17/2012
## 6 BR2 - Bridge Creek Gable 7/17/2012 3/28/2018
## 7 BR3 - Bridge Creek Ranch 7/17/2012 11/6/2018
## 8 JDC - Cottonwood Creek, NF John Day 9/7/2018
## 9 MJ1 - Middle Fork John Day Array 11/6/2013
## 10 SJ1 - SF John Day (Mid) 7/17/2012
## 11 SJ2 - SF John Day (Murderer's) 7/17/2012
## 12 JDM - Upper John Day River Array 12/14/2015
## Interrogation.Site.Location.RKM
## 1 351.032
## 2 351.034.002
## 3 351.134.001
## 4 351.218.002
## 5 351.218.014
## 6 351.218.022
## 7 351.218.027
## 8 351.298.025.001
## 9 351.298.052.068
## 10 351.341.010
## 11 351.341.027
## 12 351.347Is there reason to believe that the detection efficiency of the antennas at the river mouth site may have changed over time?
Yes, given Shelby’s observations and notes from the event log. Shift in 2012.
Two eras:
1.2007-2011 2. 2012-present
JD1 description from PTAGIS:
John Day River in-stream detection, near McDonald Ferry at RM 20.
JD1 operational history notes from PTAGIS
Nothing of significance
Detection efficiency
| year | missed_det | total | det_eff | det_eff_lower95 | det_eff_upper95 |
|---|---|---|---|---|---|
| 2010 | 0 | 1 | 1.000 | 0.025 | 1.000 |
| 2012 | 0 | 12 | 1.000 | 0.735 | 1.000 |
| 2013 | 23 | 61 | 0.623 | 0.490 | 0.744 |
| 2014 | 63 | 113 | 0.442 | 0.349 | 0.539 |
| 2015 | 73 | 112 | 0.348 | 0.261 | 0.444 |
| 2016 | 69 | 86 | 0.198 | 0.120 | 0.298 |
| 2017 | 13 | 25 | 0.480 | 0.278 | 0.687 |
| 2018 | 13 | 22 | 0.409 | 0.207 | 0.636 |
| 2019 | 3 | 16 | 0.812 | 0.544 | 0.960 |
| 2020 | 19 | 46 | 0.587 | 0.432 | 0.730 |
| 2021 | 17 | 26 | 0.346 | 0.172 | 0.557 |
| 2022 | 14 | 15 | 0.067 | 0.002 | 0.319 |
| Total | 307 | 535 | 0.426 | 0.384 | 0.469 |
USGS data
Station: John Day River at Mcdonald Ferry, OR USGS 14048000 - discharge only
## [[1]]
##
## [[2]]
Detection efficiency vs. discharge
det_eff_glm(variables = "discharge only",
tributary_name = "John Day River",
usgs_file_name = "john_day_river_14048000.txt",
equipment_categories_start_run_years = NA,
equipment_categories_end_run_years = NA,
river_mouth_site = "JD1 - John Day River, McDonald Ferry",
river_mouth_site_start_date = "2007-09-01", river_mouth_site_end_date = "2023-01-01")## [[1]]
##
## Call:
## glm(formula = detected ~ mean_discharge_cfs, family = binomial(link = "logit"),
## data = trib_det_discharge)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.069 -1.055 -1.051 1.306 1.313
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -3.466e-01 4.109e-01 -0.843 0.399
## mean_discharge_cfs 2.983e-05 2.439e-04 0.122 0.903
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 729.96 on 534 degrees of freedom
## Residual deviance: 729.94 on 533 degrees of freedom
## AIC: 733.94
##
## Number of Fisher Scoring iterations: 4
##
##
## [[2]]
Methow River
- I don’t know what’s going on with MRB site - it seems like potentially an aggregation of all sites prior 2004-2008
- LMR site - moved in 2017
- Seems like we would definitely need to calculate different detection efficiencies for different time periods
## event_site_name Int.Site.Start.Date Int.Site.End.Date
## 1 MRB - Methow River Basin 9/15/2004 1/1/2009
## 2 LMR - Lower Methow River at Pateros 3/1/2009
## 3 LMR - Lower Methow River at Pateros 3/1/2009
## 4 GLC - Gold Creek, Methow River 1/1/2009
## 5 LBC - Libby Creek, Methow River 1/1/2009
## 6 MRC - Methow River at Carlton 9/21/2015
## 7 BVC - Beaver Creek, Methow River 1/1/2009
## 8 BVC - Beaver Creek, Methow River 1/1/2009
## 9 TWR - Lwr Twisp Rvr near MSRF Ponds 7/15/2008
## 10 LTP - Lower Twisp Acclimation Pond 3/15/2011
## 11 LBT - Little Bridge Creek (Twisp R.) 6/1/2012 6/9/2015
## 12 MRT - Methow River at Twisp 9/28/2009 8/25/2016
## 13 18N - 1890s Channel Methow River 11/2/2015 12/9/2019
## 14 M3R - 3R side channel Methow River 11/4/2014 10/8/2018
## 15 MWF - Whitefish SC in Methow River 12/17/2013 10/8/2018
## 16 CRW - Chewuch River above Winthrop 4/1/2010
## 17 CWP - Chewuch Acclimation Pond 4/16/2015
## 18 CRU - Upper Chewuch Instream Array 7/28/2014
## 19 SCP - Spring Creek Acclimation Pond 3/1/2008
## 20 MRW - Methow River at Winthrop 9/21/2009
## 21 MSH - Methow Fish Hatchery Outfall 4/15/2011
## 22 WFC - Wolf Creek, Methow River 12/1/2008
## 23 MVP - Mid-Valley Acclimation Pond 3/23/2012
## 24 HSL - Hancock Springs Lower 4/17/2013 1/6/2016
## 25 HSU - Hancock Springs Upper 4/17/2013 1/6/2016
## 26 HSM - Hancock Springs Middle 4/17/2013 1/4/2016
## 27 EWC - Early Winters Creek rkm 0.36 4/1/2013 9/6/2017
## 28 LOR - Lost River at rkm 0.81 3/22/2013 8/18/2017
## Interrogation.Site.Location.RKM
## 1
## 2 843.003
## 3 843.008
## 4 843.035.001
## 5 843.042.001
## 6 843.045
## 7 843.057.001
## 8 843.057.003
## 9 843.066.002
## 10 843.066.002
## 11 843.066.014.001
## 12 843.067
## 13 843.067.000
## 14 843.075
## 15 843.076
## 16 843.080.001
## 17 843.080.010
## 18 843.080.028
## 19 843.081
## 20 843.085
## 21 843.085
## 22 843.085.001
## 23 843.088
## 24 843.097.001
## 25 843.097.001
## 26 843.097.001
## 27 843.113.001
## 28 843.122.001Is there reason to believe that the detection efficiency of the antennas at the river mouth site may have changed over time?
Yes, when the site moved in 2017. However, there are also lots of outages/issues in 2010-2014.
Two eras:
- 2009-7/31/2017
- 8/1/2017-present
LMR description from PTAGIS:
LMR is a permanent instream PIT tag interrogation site on the Methow River. When first installed with a single row of six antennas, it was located near the WDFW Miller Hole access site at about river kilometer 3. In December 2010, a second row of six antennas was added to the site. In August 2017, the site was relocated 5 kilometers upstream and the two FS1001M transceivers were replaced with a single Biomark/QST QuBe controller. The site currently consists of two rows of antennas, with each row nearly spanning the wetted width of the channel during base flows. Each row consists of six 20-foot HDPE antennas, installed in flat-plate configuration. Each antenna is powered by a Biomark IS1001 (ACN) and the ACNs are connected to a Biomark/QST QuBe controller. The antennas were built and installed by WDFW. The site is powered by a thermoelectric generator. LMR has remote communication abilities provided by a cellular modem. A submersible pressure transducer and temperature probe sensor are also installed to provide environmental condition data collection.
LMR operational history notes from PTAGIS
- 2017: Site moved 5 km upstream and both Mux transceivers were replaced with a QuBE/IS1001 setup Start and end dates based on timer tags.
- 2014: Data lost from B antennas April 23-28. Data lost from A antennas May 6-8. Data lost from B antennas May 17-27. Site down from July 17-September 3 due to wildfire.
- 2012: Multiple periods when one or more antennas were not functioning or data was lost. Check event log for details.
- 2011: Array A1-A6, which had been disabled since Dec. 15, 2010, was restored on January 4, 2011. Array C1-C6 was brought back online on March 4. Site down Apr. 8 - Apr. 9. Antenna B3 stopped working on May 15. Antennas B4-B6 stopped working on May 22. Antennas A4-A6 stopped working on May 24. Antenna A3 stopped working on June 4. Antennas A1 and B2 stopped working on June 7. Only antennas A2 and B1 functioning as of June 7. Antennas A1, A3, A4, A5, B2, B3, B4, B5 reinstalled September 27. All antennas, except A6 and B6, installed and operational as of 1400 September 27.
- 2010: Refer to the LMR event log for details about individual antenna outages between January 1 and June 21. The entire site was out of service between June 21 and August 23. A second array was installed on Dec. 2, immediately below the original array. The original (A0) array failed on Dec. 14 and the new array (B0) failed on Dec. 15.
Detection efficiency
| year | missed_det | total | det_eff | det_eff_lower95 | det_eff_upper95 |
|---|---|---|---|---|---|
| 2009 | 14 | 43 | 0.674 | 0.515 | 0.809 |
| 2010 | 7 | 32 | 0.781 | 0.600 | 0.907 |
| 2011 | 12 | 33 | 0.636 | 0.451 | 0.796 |
| 2012 | 41 | 106 | 0.613 | 0.514 | 0.706 |
| 2013 | 31 | 87 | 0.644 | 0.534 | 0.744 |
| 2014 | 13 | 75 | 0.827 | 0.722 | 0.904 |
| 2015 | 18 | 81 | 0.778 | 0.672 | 0.863 |
| 2016 | 26 | 94 | 0.723 | 0.622 | 0.811 |
| 2017 | 9 | 40 | 0.775 | 0.615 | 0.892 |
| 2018 | 17 | 49 | 0.653 | 0.504 | 0.783 |
| 2019 | 5 | 31 | 0.839 | 0.663 | 0.945 |
| 2020 | 4 | 43 | 0.907 | 0.779 | 0.974 |
| 2021 | 12 | 75 | 0.840 | 0.737 | 0.915 |
| 2022 | 8 | 19 | 0.579 | 0.335 | 0.797 |
| Total | 217 | 808 | 0.731 | 0.699 | 0.762 |
USGS data
Station: Methow River near Pateros, WA USGS 12449950 - discharge and gage height
## Warning in mask$eval_all_mutate(quo): NAs introduced by coercion## [[1]]
##
## [[2]]
##
## [[3]]
##
## [[4]]## Warning: Removed 165 rows containing missing values (geom_point).
Detection efficiency vs. discharge
det_eff_glm(variables = "discharge and gage height",
tributary_name = "Methow River",
usgs_file_name = "methow_river_12449950.txt",
equipment_categories_start_run_years = c("09/10", "17/18"),
equipment_categories_end_run_years = c("16/17", "21/22"),
river_mouth_site = "LMR - Lower Methow River at Pateros",
river_mouth_site_start_date = "2009-03-01", river_mouth_site_end_date = "2023-01-01")## Warning in mask$eval_all_mutate(quo): NAs introduced by coercion## [[1]]
##
## Call:
## glm(formula = detected ~ era + mean_discharge_cfs, family = binomial(link = "logit"),
## data = trib_det_discharge)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.8926 -1.3862 0.6753 0.8246 0.9820
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 2.3718642 0.4265411 5.561 2.69e-08 ***
## era17/18-21/22 0.1925972 0.1803057 1.068 0.285444
## mean_discharge_cfs -0.0007725 0.0002152 -3.589 0.000332 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 939.60 on 806 degrees of freedom
## Residual deviance: 922.72 on 804 degrees of freedom
## AIC: 928.72
##
## Number of Fisher Scoring iterations: 4
##
##
## [[2]]
Okanogan River
- No river mouth site, but one on Lower Okanogan (OKL) at RKM 25. File says it started 3/1/2013, PTAGIS says it started 10/8/2013.
## event_site_name Int.Site.Start.Date Int.Site.End.Date
## 1 OKL - Lower Okanogan Instream Array 3/15/2013
## 2 LLC - Loup Loup Creek Instream Array 3/7/2013
## 3 SA1 - Salmon Creek Instream Array 2/8/2011
## 4 SA1 - Salmon Creek Instream Array 2/8/2011
## 5 SA0 - Salmon Creek below OID Div. 2/1/2016
## 6 OMK - Omak Creek Instream Array 1/1/2006
## 7 OBF - Omak Creek below Mission Falls 2/1/2016
## 8 OMF - Omak Creek above Mission Falls 3/3/2015
## 9 WAN - Wanacut Creek 3/1/2014
## 10 JOH - Johnson Creek 3/1/2014
## 11 JOH - Johnson Creek 3/1/2014
## 12 TNK - Tunk Creek Instream Array 3/1/2014
## 13 AEN - Aeneas Creek Temporary Array 3/1/2014
## 14 BPC - Bonaparte Creek Instream Array 1/17/2013
## 15 ANT - Antoine Creek Instream Array 11/9/2009
## 16 WHS - Wildhorse Spring Creek 3/1/2014
## 17 ZSL - Zosel Dam Combined 9/1/2010
## 18 TON - Tonasket Creek 3/1/2014
## 19 NMC - Ninemile Creek Instream Array 2/12/2011
## 20 OKI - Inkaneep Creek 4/27/2015
## 21 OKC - Okanagan Channel at VDS-3 11/6/2009
## 22 OKV - Vasuex Creek, BC, Canada 3/23/2018
## Interrogation.Site.Location.RKM
## 1 858.025
## 2 858.028.001
## 3 858.041.002
## 4 858.041.003
## 5 858.041.006
## 6 858.052.000
## 7 858.052.011
## 8 858.052.012
## 9 858.057.001
## 10 858.066.001
## 11 858.066.001
## 12 858.073.001
## 13 858.086.001
## 14 858.092.001
## 15 858.099.000
## 16 858.114.001
## 17 858.132
## 18 858.133.001
## 19 858.134.001
## 20 858.139.001
## 21 858.149
## 22 858.163.001Is there reason to believe that the detection efficiency of the antennas at the river mouth site may have changed over time?
There are some odd things in the event log about noise, but no directional/era changes. Should calculate annual detection efficiencies and see if there are significant changes.
OKL description from PTAGIS:
OKL is a permanent instream PIT tag interrogation site at RKM 24.9 on the mainstem Okanogan River, upstream of Chiliwist area in Okanogan County. The site consists of two rows of antennas, with each row spanning the wetted width of the channel during base flows. Each row consists of six 20-foot PVC antennas, installed in flat-plate configuration. The antennas were built and installed by WDFW and CCT. The site is powered by a thermoelectric generator. OKL has remote communication abilities provided by a cellular modem and Campbell Scientific CR1000 datalogger system. A submersible pressure transducer and temperature probe sensors are also installed to provide environmental condition data collection.
OKL operational history notes from PTAGIS
- 2014: Several unexplained gaps in data collection during January and March.
Detection efficiency
| year | missed_det | total | det_eff | det_eff_lower95 | det_eff_upper95 |
|---|---|---|---|---|---|
| 2013 | 62 | 69 | 0.101 | 0.042 | 0.198 |
| 2014 | 43 | 103 | 0.583 | 0.481 | 0.679 |
| 2015 | 30 | 82 | 0.634 | 0.520 | 0.738 |
| 2016 | 33 | 60 | 0.450 | 0.321 | 0.584 |
| 2017 | 10 | 24 | 0.583 | 0.366 | 0.779 |
| 2018 | 33 | 54 | 0.389 | 0.259 | 0.531 |
| 2019 | 14 | 22 | 0.364 | 0.172 | 0.593 |
| 2020 | 5 | 20 | 0.750 | 0.509 | 0.913 |
| 2021 | 12 | 22 | 0.455 | 0.244 | 0.678 |
| 2022 | 7 | 10 | 0.300 | 0.067 | 0.652 |
| Total | 249 | 466 | 0.466 | 0.420 | 0.512 |
USGS data
Station: Okanogan River at Malott, WA USGS 12447200 - discharge and gage height
## [[1]]
##
## [[2]]
##
## [[3]]
##
## [[4]]## Warning: Removed 130 rows containing missing values (geom_point).
Detection efficiency vs. discharge
det_eff_glm(variables = "discharge and gage height",
tributary_name = "Okanogan River",
usgs_file_name = "okanogan_12447200.txt",
equipment_categories_start_run_years = NA,
equipment_categories_end_run_years = NA,
river_mouth_site = "OKL - Lower Okanogan Instream Array",
river_mouth_site_start_date = "2013-03-15", river_mouth_site_end_date = "2023-01-01")## [[1]]
##
## Call:
## glm(formula = detected ~ mean_discharge_cfs, family = binomial(link = "logit"),
## data = trib_det_discharge)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.4920 -1.0348 -0.6319 1.0788 1.8490
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 3.4456038 0.6060601 5.685 1.31e-08 ***
## mean_discharge_cfs -0.0009886 0.0001667 -5.929 3.04e-09 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 643.81 on 465 degrees of freedom
## Residual deviance: 603.67 on 464 degrees of freedom
## AIC: 607.67
##
## Number of Fisher Scoring iterations: 4
##
##
## [[2]]
Salmon River
Tons of sites, but all on tribtuaries/different forks of the Salmon
## event_site_name Int.Site.Start.Date Int.Site.End.Date
## 1 SFG - SF Salmon at Guard Station Br. 3/1/2009
## 2 ZEN - Secesh River at Zena Cr. Ranch 3/1/2009
## 3 ESS - EFSF Salmon River at Parks Cr. 3/1/2009
## 4 KRS - SF Salmon River at Krassel Cr. 1/22/2008
## 5 TAY - Big Creek at Taylor Ranch 7/1/2006
## 6 TAY - Big Creek at Taylor Ranch 7/1/2006
## 7 PCA - Panther Creek Array 7/27/2017
## 8 NFS - North Fork Salmon River 11/18/2015
## 9 NFS - North Fork Salmon River 11/18/2015
## 10 CRC - Carmen Creek, Salmon R. Basin 10/21/2013 3/1/2018
## 11 LLR - Lower Lemhi River 8/1/2009
## 12 EVL - Eagle Valley Ranch - Lower 8/5/2019
## 13 S2O - Lemhi Sub-reach 2 SC Outlet 6/29/2017 3/20/2019
## 14 BHC - Bohannon Creek Lemhi R Basin 10/6/2011
## 15 BHC - Bohannon Creek Lemhi R Basin 10/6/2011
## 16 S2I - Lemhi Sub-reach 2 SC Inlet 6/29/2017 6/14/2019
## 17 EVU - Eagle Valley Ranch - Upper 7/18/2019
## 18 WPC - Wimpey Creek, Lemhi R. Basin 10/9/2013 4/26/2018
## 19 KEN - Kenney Creek In-stream Arrays 6/1/2010
## 20 KEN - Kenney Creek In-stream Arrays 6/1/2010
## 21 KEN - Kenney Creek In-stream Arrays 6/1/2010
## 22 AGC - Agency Creek, Lemhi R. Basin 10/21/2013 11/6/2016
## 23 HYC - Hayden Creek In-stream Array 8/1/2009
## 24 LRW - Lemhi River Weir 8/1/2009
## 25 LLS - Lemhi Little Springs Instream 6/14/2011
## 26 USE - Upper Salmon River at rkm 437 9/12/2012
## 27 USI - Upper Salmon River at rkm 460 8/30/2012
## 28 YFK - Yankee Fork Salmon River 3/29/2012
## 29 CEY - Cearley Creek Side Channel 1/1/2016 11/20/2018
## 30 VC2 - Valley Creek, Downstream Site 7/10/2002
## 31 VC1 - Valley Creek, Upstream Site 7/10/2002 8/9/2021
## 32 RFL - Redfish Lake Creek 4/1/2018
## 33 STL - Sawtooth Hatchery Adult Trap 12/1/2009 8/5/2018
## Interrogation.Site.Location.RKM
## 1 522.303.215.030
## 2 522.303.215.059.003
## 3 522.303.215.060.021
## 4 522.303.215.065
## 5 522.303.319.029.011
## 6 522.303.319.029.011
## 7 522.303.338.005
## 8 522.303.381.001
## 9 522.303.381.002
## 10 522.303.408.001
## 11 522.303.416.001
## 12 522.303.416.016
## 13 522.303.416.017
## 14 522.303.416.017.001
## 15 522.303.416.017.001
## 16 522.303.416.018
## 17 522.303.416.020
## 18 522.303.416.020.001
## 19 522.303.416.029.000
## 20 522.303.416.029.000
## 21 522.303.416.029.000
## 22 522.303.416.039.001
## 23 522.303.416.049.001
## 24 522.303.416.050
## 25 522.303.416.066.000
## 26 522.303.437
## 27 522.303.460
## 28 522.303.591.003
## 29 522.303.591.009
## 30 522.303.609.001
## 31 522.303.609.002
## 32 522.303.615.001
## 33 522.303.617.000Tucannon River
- LTR at RKM 3, active October 2005
## event_site_name Int.Site.Start.Date Int.Site.End.Date
## 1 LTR - Lower Tucannon River 10/13/2005
## 2 MTR - Middle Tucannon River 9/23/2011
## 3 UTR - Upper Tucannon River 10/19/2011
## 4 TFH - Tucannon Fish Hatchery 2/4/2012
## Interrogation.Site.Location.RKM
## 1 522.100.003
## 2 522.100.019
## 3 522.100.053
## 4 522.100.059Is there reason to believe that the detection efficiency of the antennas at the river mouth site may have changed over time?
There has been a lot of change with this site, and long periods of inactivity as well as multiple shorter periods. Should calculate annual percentages and investigate. Shelby calculated detection efficiencies for 07/07 through 14/15, with gap for 08/09 due to data loss. 06/07 and 07/08 detection efficiencies were above 96%; 09/10 onward there seems to be a drop all the way down to around 60% in 14/15.
Three potential eras:
- August 2020-present
- 2005-1/8/2009
- Inactive: 1/8/2009-9/10/2009
However - we only have data from 2011 onwards. So our eras will be:
- 10/11 through 19/20
- 20/21 - present
LTR description from PTAGIS:
LTR is a permanent instream PIT tag interrogation site at RKM 2.5 on the Tucannon River. The current configuration installed August 2020 consists of three rows of antennas. The upstream row consists of 2 20-foot HDPE antennas, the middle row consists of 2 20 foot HDPE antennas and 1 10 foot PVC antenna, the bottom row consists of 2 HDPE antennas, installed in flat-plate configuration. Each antenna is powered by a Biomark Multiplexing Reader IS1001-MC master controller. The antennas were built and installed by WDFW. The electrical power at the site is provided by 6 200 watt solar panels. Data currently will be downloaded by Biomark through a satellite modem. No environmental monitors are installed at this time. This site has variously consisted of one or two groups of arrays, about a kilometer apart, located near the mouth of the Tucannon River. From Oct. 2005 until April 2008 the downstream array group consisted of two tandem “log” antenna arrays that spanned the low-water channel above the boat ramp. The upstream array group was located at an abandoned railroad bridge abutment upstream of Hwy 261 on the Tucannon River downstream from Starbuck. The upstream array (A0) operated from Oct. 2005 until January 2009. Its various configurations included both pass-through and pass-over antennas. A single array (C0) with six PVC pipe antennas powered by a QST Qube was re-deployed above the boat ramp in Sept. 2009. Responsibility for site operations transferred from USFWS to WDFW on Jan. 7, 2010. The C0 in-stream array was relocated below the Hwy 261 bridge on Sept. 29, 2010. The Qube was replaced with a Biomark IS1001-MC November 2018.
LTR operational history notes from PTAGIS
- 2011: Site down from February 24-28 and April 3-12. High flows caused various antennas to lose power or have high noise throughout the season - see event logs for details. Three antennas were replaced August 16, but not fully functional until August 29.
- 2010: Data collected prior to Jan. 7 were lost due to an equipment failure. No data are available between Jan. 19 and Feb. 4 due to a complete loss of power and failure of the lithium battery. No data are available between Feb. 16-18, Apr. 16-21, or May 10-24 due to loss of buffered records. No data available between Sept. 1-20; propane ran out. Detectors were moved upstream near the Hwy 261 bridge on Sept. 29, 2010. No data between Dec. 1-13 due to a TEG malfunction.
- 2009: The original A0 MUX array was washed out on Jan. 8, 2009. The downstream antennas in the Tucannon River (identified by transceiver C0) were reinstalled on September 10. These antennae replace the upstream array (transceiver A0) that was blown out. The configuration of the new antenna array is as follows, looking downstream: Beginning on the left hand streambank is C1, C2, and C3 (C3 is approximately mid stream). Slightly downstream (approx. 2 feet) beginning mid stream and going towards the right hand streambank are C4, C5 and C6. There is overlap of C2 and C3 with C4 and C5. Data collected between Nov. 22, 2009 and Jan. 7, 2010 were lost due to an equipment failure.
Detection efficiency
| year | missed_det | total | det_eff | det_eff_lower95 | det_eff_upper95 |
|---|---|---|---|---|---|
| 2011 | 0 | 25 | 1.000 | 0.863 | 1.000 |
| 2012 | 16 | 89 | 0.820 | 0.725 | 0.894 |
| 2013 | 3 | 47 | 0.936 | 0.825 | 0.987 |
| 2014 | 28 | 67 | 0.582 | 0.455 | 0.702 |
| 2015 | 25 | 64 | 0.609 | 0.479 | 0.729 |
| 2016 | 9 | 70 | 0.871 | 0.770 | 0.940 |
| 2017 | 7 | 25 | 0.720 | 0.506 | 0.879 |
| 2018 | 29 | 51 | 0.431 | 0.293 | 0.578 |
| 2019 | 16 | 34 | 0.529 | 0.351 | 0.702 |
| 2020 | 7 | 16 | 0.562 | 0.299 | 0.802 |
| 2021 | 1 | 24 | 0.958 | 0.789 | 0.999 |
| 2022 | 0 | 28 | 1.000 | 0.877 | 1.000 |
| Total | 141 | 540 | 0.739 | 0.700 | 0.775 |
USGS data
Station: Tucannon River near Starbuck, WA USGS 13344500 - discharge and gage height
## [[1]]
##
## [[2]]
##
## [[3]]
##
## [[4]]## Warning: Removed 4 rows containing missing values (geom_point).
Detection efficiency vs. discharge
det_eff_glm(variables = "discharge and gage height",
tributary_name = "Tucannon River",
usgs_file_name = "tucannon_river_13344500.txt",
equipment_categories_start_run_years = c("10/11", "20/21"),
equipment_categories_end_run_years = c("19/20", "21/22"),
river_mouth_site = "LTR - Lower Tucannon River",
river_mouth_site_start_date = "2005-10-13", river_mouth_site_end_date = "2023-01-01")## [[1]]
##
## Call:
## glm(formula = detected ~ era + mean_discharge_cfs, family = binomial(link = "logit"),
## data = trib_det_discharge)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -2.8219 -1.5322 0.7711 0.8354 0.8601
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.470475 0.501504 0.938 0.34818
## era20/21-21/22 3.124789 1.016359 3.074 0.00211 **
## mean_discharge_cfs 0.002366 0.002688 0.880 0.37866
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 620.15 on 539 degrees of freedom
## Residual deviance: 592.78 on 537 degrees of freedom
## AIC: 598.78
##
## Number of Fisher Scoring iterations: 6
##
##
## [[2]]## Warning in max(ids, na.rm = TRUE): no non-missing arguments to max; returning
## -Inf
Umatilla River
- TMF combined at RKM 5, active Nov 2006
- TMA adult fishway was separate until Nov 2006
## event_site_name Int.Site.Start.Date Int.Site.End.Date
## 1 TMF - Three Mile Falls Dam Combined 11/8/2006
## 2 TMJ - 3-Mile Falls Dam Smolt Bypass 3/9/1999 7/12/2006
## 3 TMA - 3-Mile Falls Dam Adult Fishway 3/7/2002 11/8/2006
## 4 UMW - Umatilla R Recycled Water Fac 1/8/2018
## 5 MWC - Maxwell Canal 3/1/2007
## 6 FDD - Feed Diversion Dam 11/1/2008
## 7 UMF - Umatilla R below Feed Dam 1/8/2018 4/8/2019
## 8 FDC - Feed Canal 12/5/2006
## 9 UM2 - Umatilla River Instream Array 8/1/2007 8/11/2010
## 10 UM1 - Umatilla River USFWS 10/20/2004 3/20/2011
## Interrogation.Site.Location.RKM
## 1 465.005
## 2 465.005
## 3 465.005
## 4 465.009
## 5 465.024
## 6 465.045
## 7 465.045
## 8 465.047
## 9 465.124
## 10 465.145.000Is there reason to believe that the detection efficiency of the antennas at the river mouth site may have changed over time?
There’s nothing really concerning at the TMF site. Shelby calculated detection efficiencies in some years, and they varied a lot, from 54% to 100%. But also seems like there wasn’t a ton of data.
TMF description from PTAGIS:
Adult Fishway and Juvenile Bypass/subsampling facility at Three Mile Falls Dam
TMF operational history notes from PTAGIS
- 2006: First year for TMF site, which combines and replaces the previous TMJ and TMA sites.
Detection efficiency
| year | missed_det | total | det_eff | det_eff_lower95 | det_eff_upper95 |
|---|---|---|---|---|---|
| 2007 | 2 | 3 | 0.333 | 0.008 | 0.906 |
| 2008 | 4 | 9 | 0.556 | 0.212 | 0.863 |
| 2009 | 6 | 15 | 0.600 | 0.323 | 0.837 |
| 2010 | 6 | 10 | 0.400 | 0.122 | 0.738 |
| 2011 | 7 | 9 | 0.222 | 0.028 | 0.600 |
| 2012 | 8 | 13 | 0.385 | 0.139 | 0.684 |
| 2013 | 17 | 28 | 0.393 | 0.215 | 0.594 |
| 2014 | 2 | 32 | 0.938 | 0.792 | 0.992 |
| 2015 | 7 | 48 | 0.854 | 0.722 | 0.939 |
| 2016 | 7 | 25 | 0.720 | 0.506 | 0.879 |
| 2017 | 0 | 6 | 1.000 | 0.541 | 1.000 |
| 2018 | 2 | 38 | 0.947 | 0.823 | 0.994 |
| 2019 | 3 | 17 | 0.824 | 0.566 | 0.962 |
| 2020 | 0 | 22 | 1.000 | 0.846 | 1.000 |
| 2021 | 0 | 18 | 1.000 | 0.815 | 1.000 |
| 2022 | 0 | 6 | 1.000 | 0.541 | 1.000 |
| Total | 71 | 299 | 0.763 | 0.710 | 0.810 |
USGS data
Note - since the tributary site in this case is at a dam, I don’t expet river stage/flow to make a big difference in detection probability.
Station: Umatilla River near Umatilla, OR USGS 14033500 - discharge only
## [[1]]
##
## [[2]]
Detection efficiency vs. discharge
det_eff_glm(variables = "discharge only",
tributary_name = "Umatilla River",
usgs_file_name = "umatilla_river_14033500.txt",
equipment_categories_start_run_years = NA,
equipment_categories_end_run_years = NA,
river_mouth_site = "TMF - Three Mile Falls Dam Combined",
river_mouth_site_start_date = "2006-11-08", river_mouth_site_end_date = "2023-01-01")## [[1]]
##
## Call:
## glm(formula = detected ~ mean_discharge_cfs, family = binomial(link = "logit"),
## data = trib_det_discharge)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.7532 0.6959 0.7122 0.7491 0.8410
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.4547292 0.4277236 3.401 0.000671 ***
## mean_discharge_cfs -0.0005171 0.0007221 -0.716 0.473960
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 327.78 on 298 degrees of freedom
## Residual deviance: 327.28 on 297 degrees of freedom
## AIC: 331.28
##
## Number of Fisher Scoring iterations: 4
##
##
## [[2]]
Walla Walla River
- ORB at RKM 10, active April 2005 - May 2015
- PRV at RKM 9, active September 2012 - April 2019
- WWB at RKM 5, active April 2019 - present
## event_site_name Int.Site.Start.Date Int.Site.End.Date
## 1 WWB - Walla Walla River Barge Array 4/11/2019
## 2 PRV - Walla Walla R at Pierce RV Prk 9/25/2012 4/8/2019
## 3 ORB - Oasis Road Bridge 4/15/2005 5/4/2015
## 4 HST - Touchet River at Harvey Shaw 9/1/2015
## 5 BBT - Touchet River at Bolles Bridge 11/1/2011
## 6 COP - Lower Coppei Instream Array 10/15/2015
## 7 JPT - Juvenile Pond Touchet 7/12/2016
## 8 JPT - Juvenile Pond Touchet 7/12/2016
## 9 PAT - Pattit Creek Instream Site 11/17/2016
## 10 MDR - McDonald Road Bridge 9/25/2012 1/14/2018
## 11 LWD - Lowden Diversion Dam 11/29/2007 10/24/2013
## 12 MCD - Mill Creek Diversion Project 2/25/2005 12/8/2021
## 13 KCB - Kiwanis Camp Bridge, Mill C 4/16/2005 4/1/2011
## 14 MCI - Mill Creek Intake Dam 6/1/2011 2/2/2017
## 15 BGM - Burlingame Dam and Canal 10/30/2006
## 16 YHC - Yellowhawk Creek 12/1/2006
## 17 NBA - Nursery Bridge Adult 10/3/2003
## 18 NFW - North Fork Walla Walla River 5/18/2012 4/19/2013
## 19 WW1 - Harris Bridge S F Walla Walla 9/3/2002 2/5/2020
## 20 WW2 - SF Walla Walla at Bear Creek 9/3/2002 2/5/2020
## Interrogation.Site.Location.RKM
## 1 509.005
## 2 509.009
## 3 509.010
## 4 509.035.050
## 5 509.035.065
## 6 509.035.082.001
## 7 509.035.087
## 8 509.035.087
## 9 509.035.101.001
## 10 509.041
## 11 509.051
## 12 509.054.019
## 13 509.054.035
## 14 509.054.041
## 15 509.059
## 16 509.063.013
## 17 509.072
## 18 509.081.001
## 19 509.081.013
## 20 509.081.021Is there reason to believe that the detection efficiency of the antennas at the river mouth site may have changed over time?
There are three different river mouth arrays that are used, depending on the timeframe:
- ORB: 4/15/2005-5/4/2015
- PRV: 9/25/2012-4/8/2019
- WWB: 4/11/2019-present
Shelby calculated detection efficiencies at ORB 07/08-11/12, PRV 12/13-14/15. ORB does seem to have lower, with high SE, detection efficiencies. PRV has generally higher detection efficiencies.
For each of these sites, there are no major shifts in equipment besides a few periods where antennas were down to be aware of.
WWB description from PTAGIS:
The site consists of two 50 ft wide floating barges with twelve 6 ft verticle fins. Each pair of fins act as a single antenna, detection for each antenna is the full length of the fin (6 ft) and 3 ft fore and aft of each fin. Barge will be held in place by single 250lb Danforth anchor. Electronics are powered by battery and solar, cellular modems are used for remote access. Site was initially configured with transceiver and antenna IDs opposite to PTAGIS convention, but was corrected on May 16, 2019.
WWB operational history notes from PTAGIS
Site was down 2/10/2020-2/28/2020 due to flooding.
ORB description from PTAGIS:
In-stream arrays at Oasis Road Bridge, lower Walla Walla River
ORB operational history notes from PTAGIS
- 2011: Antennas 1-5 lost power and or anchoring between Jan. 15 and Jan 18, only antenna 6 still working. As of Feb. 3, antennas 4, 5 and 6 are working. Site down from June 2 - 6 due to power loss from vandalization. Only antennas 5 and 6 working as of May 27. All antennas repaired and fully functioning as of September 1.
- 2009: 5/18/09 to 5/27/09 - MUX transceiver locked up; no data for this time period. 9/25/09 to 10/05/09 - Site down for maintenance; no data were collected.
- 2006: All antennas were out of service between January 1 and January 25, due to a high water event. Various antennas were in and out of service after January 25. See the ORB event log for additional details. A new Upstream Flat-Plate Array was installed on October 3, augmenting the existing Downstream Pass-Through Array.
PRV description from PTAGIS:
This interrogation site in the lower Walla Walla River at Pierce Green Valley RV Park is a flat panel, single row of 4 antennas, 3 twenty foot panels and 1 ten foot panel. This passive in-stream interrogation system is located at rkm 15 Site was removed in April 2019.
PRV operational history notes from PTAGIS
Nothing of note.
Detection efficiency - three different sites here
| year | missed_det | total | det_eff | det_eff_lower95 | det_eff_upper95 |
|---|---|---|---|---|---|
| 2019 | 3 | 7 | 0.571 | 0.184 | 0.901 |
| 2020 | 22 | 22 | 0.000 | 0.000 | 0.154 |
| 2021 | 23 | 39 | 0.410 | 0.256 | 0.579 |
| 2022 | 22 | 22 | 0.000 | 0.000 | 0.154 |
| Total | 70 | 90 | 0.222 | 0.141 | 0.322 |
| year | missed_det | total | det_eff | det_eff_lower95 | det_eff_upper95 |
|---|---|---|---|---|---|
| 2006 | 0 | 1 | 1.000 | 0.025 | 1.000 |
| 2007 | 1 | 1 | 0.000 | 0.000 | 0.975 |
| 2009 | 2 | 7 | 0.714 | 0.290 | 0.963 |
| 2010 | 8 | 26 | 0.692 | 0.482 | 0.857 |
| 2011 | 17 | 39 | 0.564 | 0.396 | 0.722 |
| 2012 | 35 | 105 | 0.667 | 0.568 | 0.756 |
| 2013 | 22 | 65 | 0.662 | 0.534 | 0.774 |
| 2014 | 72 | 88 | 0.182 | 0.108 | 0.278 |
| 2015 | 25 | 26 | 0.038 | 0.001 | 0.196 |
| Total | 182 | 358 | 0.492 | 0.439 | 0.545 |
| year | missed_det | total | det_eff | det_eff_lower95 | det_eff_upper95 |
|---|---|---|---|---|---|
| 2012 | 25 | 64 | 0.609 | 0.479 | 0.729 |
| 2013 | 4 | 54 | 0.926 | 0.821 | 0.979 |
| 2014 | 4 | 71 | 0.944 | 0.862 | 0.984 |
| 2015 | 5 | 32 | 0.844 | 0.672 | 0.947 |
| 2016 | 25 | 54 | 0.537 | 0.396 | 0.674 |
| 2017 | 1 | 32 | 0.969 | 0.838 | 0.999 |
| 2018 | 6 | 45 | 0.867 | 0.732 | 0.949 |
| 2019 | 8 | 14 | 0.429 | 0.177 | 0.711 |
| Total | 78 | 366 | 0.787 | 0.741 | 0.828 |
USGS data
Station: Walla Walla River near Touchet, WA USGS 14018500 - discharge and gage height
## [[1]]
##
## [[2]]
##
## [[3]]
##
## [[4]]## Warning: Removed 38 rows containing missing values (geom_point).
Detection efficiency vs. discharge
# WWB
det_eff_glm(variables = "discharge and gage height",
tributary_name = "Walla Walla River",
usgs_file_name = "walla_walla_14018500.txt",
equipment_categories_start_run_years = NA,
equipment_categories_end_run_years = NA,
river_mouth_site = "WWB - Walla Walla River Barge Array",
river_mouth_site_start_date = "2019-04-11", river_mouth_site_end_date = "2023-01-01")## [[1]]
##
## Call:
## glm(formula = detected ~ mean_discharge_cfs, family = binomial(link = "logit"),
## data = trib_det_discharge)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -0.7838 -0.7619 -0.7094 -0.6414 1.8343
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -2.561127 2.229699 -1.149 0.251
## mean_discharge_cfs 0.002210 0.003724 0.594 0.553
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 95.347 on 89 degrees of freedom
## Residual deviance: 94.990 on 88 degrees of freedom
## AIC: 98.99
##
## Number of Fisher Scoring iterations: 4
##
##
## [[2]]
# ORB
det_eff_glm(variables = "discharge and gage height",
tributary_name = "Walla Walla River",
usgs_file_name = "walla_walla_14018500.txt",
equipment_categories_start_run_years = NA,
equipment_categories_end_run_years = NA,
river_mouth_site = "ORB - Oasis Road Bridge",
river_mouth_site_start_date = "2005-04-15", river_mouth_site_end_date = "2015-05-04")## [[1]]
##
## Call:
## glm(formula = detected ~ mean_discharge_cfs, family = binomial(link = "logit"),
## data = trib_det_discharge)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.6185 -1.1342 -0.9353 1.2032 1.4406
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.6226470 0.3883387 -4.178 2.94e-05 ***
## mean_discharge_cfs 0.0024996 0.0005893 4.242 2.22e-05 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 496.19 on 357 degrees of freedom
## Residual deviance: 476.90 on 356 degrees of freedom
## AIC: 480.9
##
## Number of Fisher Scoring iterations: 4
##
##
## [[2]]
# PRV
det_eff_glm(variables = "discharge and gage height",
tributary_name = "Walla Walla River",
usgs_file_name = "walla_walla_14018500.txt",
equipment_categories_start_run_years = NA,
equipment_categories_end_run_years = NA,
river_mouth_site = "PRV - Walla Walla R at Pierce RV Prk",
river_mouth_site_start_date = "2012-09-25", river_mouth_site_end_date = "2019-04-08")## [[1]]
##
## Call:
## glm(formula = detected ~ mean_discharge_cfs, family = binomial(link = "logit"),
## data = trib_det_discharge)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.8353 0.6408 0.6837 0.7211 0.7360
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.8521288 0.6015563 1.417 0.157
## mean_discharge_cfs 0.0007718 0.0010052 0.768 0.443
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 379.22 on 365 degrees of freedom
## Residual deviance: 378.63 on 364 degrees of freedom
## AIC: 382.63
##
## Number of Fisher Scoring iterations: 4
##
##
## [[2]]
Wenatchee River
- LWE at RKM 2-3. PTAGIS says start date of 12/7/2010, file says 10/1/2009
## event_site_name Int.Site.Start.Date Int.Site.End.Date
## 1 LWE - Lower Wenatchee River 10/1/2009
## 2 LWE - Lower Wenatchee River 10/1/2009
## 3 MCL - Lower Mission Creek Instream 10/4/2011
## 4 WPT - White Pine Temporary Array 3/1/2011 4/27/2013
## 5 PES - Peshastin Creek 5/1/2007
## 6 UPT - Upper Peshastin Temporary Arr. 3/1/2011 6/4/2014
## 7 TCT - Tronsen Creek Temporary Array 3/1/2011 6/5/2014
## 8 CHM - Chumstick Creek 2/28/2011
## 9 BBP - Blackbird Pond Accl. Site 3/15/2012 6/30/2017
## 10 ICL - Lower Icicle Instream Array 9/8/2011
## 11 ICM - Middle Icicle Instream Array 4/1/2015
## 12 TUF - Tumwater Dam Adult Fishway 1/15/2008
## 13 MWE - Middle Wenatchee River 3/28/2008 10/14/2013
## 14 CHW - Chiwaukum Creek 4/26/2011
## 15 BVT - Beaver Creek Temporary Array 3/1/2011 8/7/2014
## 16 BVP - Beaver Creek Acclimation Pond 1/1/2006
## 17 CHL - Lower Chiwawa River 3/3/2008
## 18 CHP - Chiwawa Acc. Pond 1/1/1995
## 19 CHU - Upper Chiwawa River 4/1/2008
## 20 BMT - Big Meadow Temporary Array 3/1/2011 5/16/2014
## 21 CCT - Chikamin Creek Temporary Array 3/1/2011 5/30/2013
## 22 UCT - Upper Chiwawa Temporary Array 3/1/2011 5/12/2013
## 23 UWE - Upper Wenatchee River 10/1/2009
## 24 NAL - Lower Nason Creek 4/1/2008
## 25 BCP - Butcher Creek Acclimation Pond 1/1/2003
## 26 NAU - Upper Nason Creek 10/1/2007
## 27 RFP - Rolfing Acclimation Pond 1/1/2004
## 28 WTL - White River, Wenatchee Basin 4/1/2009
## 29 WTL - White River, Wenatchee Basin 4/1/2009
## 30 LWN - Little Wenatchee River 4/1/2009
## Interrogation.Site.Location.RKM
## 1 754.002
## 2 754.003
## 3 754.017.001
## 4 754.025.001
## 5 754.029.003
## 6 754.029.022
## 7 754.029.023.001
## 8 754.037.000
## 9 754.040
## 10 754.041.000
## 11 754.041.007
## 12 754.044
## 13 754.050
## 14 754.057.000
## 15 754.075.001
## 16 754.075.001
## 17 754.077.001
## 18 754.077.002
## 19 754.077.012
## 20 754.077.014.001
## 21 754.077.023.001
## 22 754.077.029
## 23 754.081
## 24 754.089.001
## 25 754.089.013
## 26 754.089.019
## 27 754.089.021
## 28 754.090.003
## 29 754.090.004
## 30 754.090.008.004Is there reason to believe that the detection efficiency of the antennas at the river mouth site may have changed over time?
Shelby calculated detection efficiencies for 11/12-14/15. Varied from 53.8% in 11/12 to 85% in 14/15, with single digit SEs in each year. Doesn’t seem to be directional changes.
We should start though on 01/05/2011; since that’s when site operations were restored and then kept up.
LWE description from PTAGIS:
LWE is a permanent instream PIT tag interrogation site at RKM 2.77 on the Wenatchee River. The site consists of two rows of antennas, with each row nearly spanning the wetted width of the channel during base flows. Each row consists of six 20-foot PVC antennas, installed in flat-plate configuration. Each antenna is powered by a Biomark IS1001 (ACN) and the ACNs are connected to a Biomark IS1001-MC (MTS). The antennas were built and installed by WDFW. The site is powered by a thermoelectric generator. LWE has remote communication abilities provided by a cellular modem and Campbell Scientific CR1000 datalogger. A submersible pressure transducer and temperature probe sensors are also installed to provide environmental condition data collection.
LWE operational history notes from PTAGIS
There are a number of short outages, but nothing too long term.
Detection efficiency
| year | missed_det | total | det_eff | det_eff_lower95 | det_eff_upper95 |
|---|---|---|---|---|---|
| 2011 | 92 | 144 | 0.361 | 0.283 | 0.445 |
| 2012 | 76 | 171 | 0.556 | 0.478 | 0.631 |
| 2013 | 61 | 111 | 0.450 | 0.356 | 0.548 |
| 2014 | 42 | 147 | 0.714 | 0.634 | 0.786 |
| 2015 | 27 | 119 | 0.773 | 0.687 | 0.845 |
| 2016 | 14 | 25 | 0.440 | 0.244 | 0.651 |
| 2017 | 3 | 25 | 0.880 | 0.688 | 0.975 |
| 2018 | 10 | 19 | 0.474 | 0.244 | 0.711 |
| 2019 | 3 | 21 | 0.857 | 0.637 | 0.970 |
| 2020 | 15 | 44 | 0.659 | 0.501 | 0.795 |
| 2021 | 2 | 12 | 0.833 | 0.516 | 0.979 |
| 2022 | 2 | 2 | 0.000 | 0.000 | 0.842 |
| Total | 347 | 840 | 0.587 | 0.553 | 0.620 |
USGS data
Station: Wenatchee River at Monitor, WA USGS 12462500 - discharge and gage height
## [[1]]
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## [[2]]
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## [[3]]
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## [[4]]## Warning: Removed 9 rows containing missing values (geom_point).
Detection efficiency vs. discharge
det_eff_glm(variables = "discharge and gage height",
tributary_name = "Wenatchee River",
usgs_file_name = "wenatchee_river_12462500.txt",
equipment_categories_start_run_years = NA,
equipment_categories_end_run_years = NA,
river_mouth_site = "LWE - Lower Wenatchee River",
river_mouth_site_start_date = "2011-01-05", river_mouth_site_end_date = "2023-01-01")## [[1]]
##
## Call:
## glm(formula = detected ~ mean_discharge_cfs, family = binomial(link = "logit"),
## data = trib_det_discharge)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.5815 -1.2675 0.9536 1.0446 1.1014
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 2.3276471 0.8401226 2.771 0.0056 **
## mean_discharge_cfs -0.0005705 0.0002409 -2.368 0.0179 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 1137.9 on 838 degrees of freedom
## Residual deviance: 1132.1 on 837 degrees of freedom
## AIC: 1136.1
##
## Number of Fisher Scoring iterations: 4
##
##
## [[2]]
Yakima River
- PRO at RKM 76, active October 2004
## event_site_name Int.Site.Start.Date Int.Site.End.Date
## 1 PRO - Prosser Diversion Dam Combined 10/19/2004
## 2 SAT - Lower Satus Creek 1/2/2012
## 3 TOP - Lower Toppenish Creek 1/2/2012
## 4 SM1 - Simcoe Creek at Stephensen Rd 10/31/2018
## 5 TP2 - Toppenish Creek at Simcoe Ck 11/14/2018
## 6 SUN - Sunnyside Instream Array 10/28/2015
## 7 AH1 - Ahtanum at Lasalle HS 11/15/2018
## 8 LNR - Lower Naches River 11/6/2016 5/30/2020
## 9 ROZ - Roza Diversion Dam (Combined) 3/26/1992
## 10 RZF - Roza Dam Fishway 9/1/2007 3/22/2011
## 11 TAN - Taneum Creek Instream 2/18/2010
## 12 TAN - Taneum Creek Instream 2/18/2010
## 13 SWK - Lower Swauk Creek 8/16/2011
## 14 SWK - Lower Swauk Creek 8/16/2011
## 15 LMT - Lower Mainstem Teanaway River 5/1/2010
## 16 LMT - Lower Mainstem Teanaway River 5/1/2010
## 17 NFT - North Fork Teanaway River 1/13/2012 11/30/2015
## 18 UMT - Upper main stem Teanaway River 1/13/2012 11/17/2015
## Interrogation.Site.Location.RKM
## 1 539.076
## 2 539.112.005
## 3 539.130.002
## 4 539.130.053.009
## 5 539.130.054
## 6 539.166
## 7 539.172.004
## 8 539.187.005
## 9 539.206
## 10 539.206
## 11 539.271.001
## 12 539.271.003
## 13 539.274.001
## 14 539.274.001
## 15 539.284.000
## 16 539.284.000
## 17 539.284.017.001
## 18 539.284.020Is there reason to believe that the detection efficiency of the antennas at the river mouth site may have changed over time?
Shelby calculated detection efficiencies for 07/08-14/15. Efficiencies generally very high. The arrays are in the three ladders at Prosser, so we would expect them to have higher detection efficiencies than the in stream arrays.
PRO description from PTAGIS:
This site monitors the (three) fish ladders and juvenile sampling facility at Prosser Dam. Each ladder has two antennas installed at the counting window. The juvenile sampling facility has antennas installed downstream of the separator and at the exit from the sample room.
PRO operational history notes from PTAGIS
Short periods where individual antennas were down, but no major changes.
Detection efficiency
| year | missed_det | total | det_eff | det_eff_lower95 | det_eff_upper95 |
|---|---|---|---|---|---|
| 2008 | 0 | 1 | 1.000 | 0.025 | 1.000 |
| 2009 | 1 | 7 | 0.857 | 0.421 | 0.996 |
| 2010 | 0 | 7 | 1.000 | 0.590 | 1.000 |
| 2011 | 0 | 11 | 1.000 | 0.715 | 1.000 |
| 2012 | 3 | 24 | 0.875 | 0.676 | 0.973 |
| 2013 | 0 | 10 | 1.000 | 0.691 | 1.000 |
| 2014 | 5 | 46 | 0.891 | 0.764 | 0.964 |
| 2015 | 4 | 52 | 0.923 | 0.815 | 0.979 |
| 2016 | 5 | 26 | 0.808 | 0.606 | 0.934 |
| 2017 | 1 | 25 | 0.960 | 0.796 | 0.999 |
| 2018 | 4 | 22 | 0.818 | 0.597 | 0.948 |
| 2019 | 1 | 24 | 0.958 | 0.789 | 0.999 |
| 2020 | 6 | 34 | 0.824 | 0.655 | 0.932 |
| 2021 | 0 | 27 | 1.000 | 0.872 | 1.000 |
| 2022 | 1 | 1 | 0.000 | 0.000 | 0.975 |
| Total | 31 | 317 | 0.902 | 0.864 | 0.933 |
USGS data
Note: Tributary site is in fish ladders at Prosser Dam, so we wouldn’t expect a big effect of river stage/flow.
Station: Yakima River at Kiona, WA USGS 12510500 - discharge and gage height - this station is downstream of PRO
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##
## [[3]]
##
## [[4]]## Warning: Removed 23 rows containing missing values (geom_point).
Detection efficiency vs. discharge
det_eff_glm(variables = "discharge and gage height",
tributary_name = "Yakima River",
usgs_file_name = "yakima_river_12510500.txt",
equipment_categories_start_run_years = NA,
equipment_categories_end_run_years = NA,
river_mouth_site = "PRO - Prosser Diversion Dam Combined",
river_mouth_site_start_date = "2004-10-19", river_mouth_site_end_date = "2023-01-01")## [[1]]
##
## Call:
## glm(formula = detected ~ mean_discharge_cfs, family = binomial(link = "logit"),
## data = trib_det_discharge)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -2.1575 0.4533 0.4537 0.4540 0.4542
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 2.231e+00 1.068e+00 2.088 0.0368 *
## mean_discharge_cfs -2.414e-06 2.952e-04 -0.008 0.9935
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 203.01 on 316 degrees of freedom
## Residual deviance: 203.01 on 315 degrees of freedom
## AIC: 207.01
##
## Number of Fisher Scoring iterations: 4
##
##
## [[2]]